During my ee install with --letsencrypt the install failed due in incorrect dns records. After correcting the dns records I installed letsencrypt manually using certbot. I also followed the tutorial for Weak Diffie Hellman Logjam Attack Fix. I do have https working on my domain now.

However, the nginx configuration for my domain now has entries from certbot in addition to the manual changes I made for Diffie Hellman. When I used the ee site info command it shows that SSL is disabled.

My question is can I now run ee site update --letsencrypt so that ee knows about https and the current certificates or will this break my current setup?